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<article id="content">
<header>
<h1 class="title">Module <code>Gnumed.business.gmATC</code></h1>
</header>
<section id="section-intro">
<p>ATC handling code.</p>
<p><a href="http://who.no">http://who.no</a></p>
<p>There is no DDD handling because DDD explicitly
does not carry clinical meaning.</p>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python"># -*- coding: utf-8 -*-
&#34;&#34;&#34;ATC handling code.

http://who.no

There is no DDD handling because DDD explicitly
does not carry clinical meaning.
&#34;&#34;&#34;
#============================================================
__author__ = &#34;K.Hilbert &lt;Karsten.Hilbert@gmx.net&gt;&#34;
__license__ = &#34;GPL v2 or later&#34;

import sys
import logging
import os.path
import re as regex


if __name__ == &#39;__main__&#39;:
        sys.path.insert(0, &#39;../../&#39;)
from Gnumed.pycommon import gmPG2
from Gnumed.pycommon import gmTools
from Gnumed.pycommon import gmCfgINI


_log = logging.getLogger(&#39;gm.atc&#39;)
_cfg = gmCfgINI.gmCfgData()


ATC_NICOTINE = &#39;N07BA01&#39;
ATC_ETHANOL  = &#39;V03AB16&#39;

#============================================================
def propagate_atc(substance=None, atc=None, link_obj=None):

        _log.debug(&#39;substance &lt;%s&gt;, ATC &lt;%s&gt;&#39;, substance, atc)

        if atc is not None:
                if atc.strip() == &#39;&#39;:
                        atc = None

        if atc is None:
                atcs = text2atc(text = substance, fuzzy = False, link_obj = link_obj)
                if len(atcs) == 0:
                        _log.debug(&#39;no ATC found, aborting&#39;)
                        return atc
                if len(atcs) &gt; 1:
                        _log.debug(&#39;non-unique ATC mapping, aborting&#39;)
                        return atc
                atc = atcs[0][0].strip()

        args = {&#39;atc&#39;: atc, &#39;term&#39;: substance.strip()}
        queries = [
                {&#39;cmd&#39;: &#34;UPDATE ref.substance SET atc = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc IS NULL&#34;,
                 &#39;args&#39;: args},
                {&#39;cmd&#39;: &#34;UPDATE ref.drug_product SET atc_code = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc_code IS NULL&#34;,
                 &#39;args&#39;: args}
        ]
        gmPG2.run_rw_queries(link_obj = link_obj, queries = queries)

        return atc

#============================================================
def text2atc(text=None, fuzzy=False, link_obj=None):

        text = text.strip()

        if fuzzy:
                args = {&#39;term&#39;: &#39;%%%s%%&#39; % text}
                cmd = &#34;&#34;&#34;
                        SELECT DISTINCT ON (atc_code) *
                        FROM (
                                SELECT atc as atc_code, is_group_code, pk_data_source
                                FROM ref.v_atc
                                WHERE term ilike %(term)s AND atc IS NOT NULL
                                        UNION
                                SELECT atc as atc_code, null, null
                                FROM ref.substance
                                WHERE description ilike %(term)s AND atc IS NOT NULL
                                        UNION
                                SELECT atc_code, null, null
                                FROM ref.drug_product
                                WHERE description ilike %(term)s AND atc_code IS NOT NULL
                        ) as tmp
                        ORDER BY atc_code
                &#34;&#34;&#34;
        else:
                args = {&#39;term&#39;: text.casefold()}
                cmd = &#34;&#34;&#34;
                        SELECT DISTINCT ON (atc_code) *
                        FROM (
                                SELECT atc as atc_code, is_group_code, pk_data_source
                                FROM ref.v_atc
                                WHERE lower(term) = lower(%(term)s) AND atc IS NOT NULL
                                        UNION
                                SELECT atc as atc_code, null, null
                                FROM ref.substance
                                WHERE lower(description) = lower(%(term)s) AND atc IS NOT NULL
                                        UNION
                                SELECT atc_code, null, null
                                FROM ref.drug_product
                                WHERE lower(description) = lower(%(term)s) AND atc_code IS NOT NULL
                        ) as tmp
                        ORDER BY atc_code
                &#34;&#34;&#34;

        rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])

        _log.debug(&#39;term: %s =&gt; ATCs: %s (fuzzy: %s)&#39;, text, rows, fuzzy)

        return rows

#============================================================
def exists_as_atc(substance):
        args = {&#39;term&#39;: substance}
        cmd = &#39;SELECT EXISTS (SELECT 1 FROM ref.atc WHERE lower(term) = lower(%(term)s))&#39;
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])
        return rows[0][0]

#============================================================
def get_reference_atcs(order_by=&#39;atc, term, lang&#39;):
        cmd = &#39;SELECT * FROM ref.v_atc ORDER BY %s&#39; % order_by
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd}])
        return rows

#============================================================
def atc_import(cfg_fname=None, conn=None):

        # read meta data
        _cfg.add_file_source(source = &#39;atc&#39;, file = cfg_fname, encoding = &#39;utf8&#39;)

        data_fname = os.path.join (
                os.path.dirname(cfg_fname),
                _cfg.get(group = &#39;atc&#39;, option = &#39;data file&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        )                       # must be in same dir as conf file
        version = _cfg.get(group = &#39;atc&#39;, option = &#39;version&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        lang = _cfg.get(group = &#39;atc&#39;, option = &#39;language&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        desc = _cfg.get(group = &#39;atc&#39;, option = &#39;description&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        url = _cfg.get(group = &#39;atc&#39;, option = &#39;url&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        name_long = _cfg.get(group = &#39;atc&#39;, option = &#39;long name&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        name_short = _cfg.get(group = &#39;atc&#39;, option = &#39;short name&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])

        _cfg.remove_source(source = &#39;atc&#39;)

        _log.debug(&#39;importing ATC version [%s] (%s) from [%s]&#39;, version, lang, data_fname)

        args = {&#39;ver&#39;: version, &#39;desc&#39;: desc, &#39;url&#39;: url, &#39;name_long&#39;: name_long, &#39;name_short&#39;: name_short, &#39;lang&#39;: lang}

        # find or create data source record
        cmd = u&#34;select pk from ref.data_source where name_short = %(name_short)s and version = %(ver)s&#34;
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])
        if len(rows) &gt; 0:
                data_src_pk = rows[0][0]
                _log.debug(&#39;ATC data source record existed, pk is #%s, refreshing fields&#39;, data_src_pk)
                # exists - update
                args[&#39;pk&#39;] = data_src_pk
                cmd = u&#34;&#34;&#34;UPDATE ref.data_source SET
                                name_long = %(name_long)s,
                                description = %(desc)s,
                                lang = %(lang)s,
                                source = %(url)s
                        WHERE
                                pk = %(pk)s
                &#34;&#34;&#34;
                rows = gmPG2.run_rw_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])
        else:
                _log.debug(&#39;ATC data source record not found, creating&#39;)
                # create
                cmd = u&#34;&#34;&#34;insert into ref.data_source (name_long, name_short, version, description, lang, source) values (
                        %(name_long)s,
                        %(name_short)s,
                        %(ver)s,
                        %(desc)s,
                        %(lang)s,
                        %(url)s
                ) returning pk&#34;&#34;&#34;
                rows = gmPG2.run_rw_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}], return_data = True)
                data_src_pk = rows[0][0]
                _log.debug(&#39;ATC data source record created, pk is #%s&#39;, data_src_pk)

        # import data
        csv_file = open(data_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)
        atc_reader = gmTools.unicode_csv_reader(csv_file, delimiter = &#34;,&#34;, quotechar = &#39;&#34;&#39;)

        # clean out staging area
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;delete from ref.atc_staging&#34;&#34;&#34;
        gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd}])
        curs.close()
        conn.commit()
        _log.debug(&#39;ATC staging table emptied&#39;)

        # from file into staging table
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;insert into ref.atc_staging values (%s, %s, %s, %s, %s)&#34;&#34;&#34;
        first = False
        for atc_line in atc_reader:
                # skip first
                if not first:
                        first = True
                        continue

                # skip blanks
                if atc_line[0] + atc_line[1] + atc_line[2] + atc_line[3] + atc_line[4] == &#39;&#39;:
                        continue

                comment = &#39;&#39;
                unit = &#39;&#39;
                adro = &#39;&#39;

                # &#34;1,1 mg O,P,R,...&#34;
                if regex.match(r&#39;\d{,3},\d{,3}\s.{1,2}\s.(,.)*$&#39;, atc_line[4]):
                        tmp, unit, adro = regex.split(r&#39;\s&#39;, atc_line[4])
                # &#34;1,1 mg O,P,R bezogen auf ...&#34;
                elif regex.match(r&#39;\d{,3},\d{,3}\s.{1,2}\s.(,.)*\s.+$&#39;, atc_line[4]):
                        tmp, unit, adro, comment = regex.split(r&#39;\s&#39;, atc_line[4], 3)
                # &#34;20 mg O&#34;
                elif regex.match(r&#39;\d{,3}\s.{1,2}\s.(,.)*$&#39;, atc_line[4]):
                        tmp, unit, adro = regex.split(r&#39;\s&#39;, atc_line[4])
                # &#34;20 mg O bezogen auf ...&#34;
                elif regex.match(r&#39;\d{,3}\s.{1,2}\s.(,.)*\s.+$&#39;, atc_line[4]):
                        tmp, unit, adro, comment = regex.split(r&#39;\s&#39;, atc_line[4], 3)
                # &#34;Standarddosis: 1 Tablette oder 30 ml Mixtur&#34;
                else:
                        comment = atc_line[4]

                args = [
                        atc_line[0].strip(),
                        atc_line[2],
                        unit,
                        adro,
                        comment
                ]

                gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])

        curs.close()
        conn.commit()
        csv_file.close()
        _log.debug(&#39;ATC staging table loaded&#39;)

        # from staging table to real table
        args = {&#39;src_pk&#39;: data_src_pk}
        queries = []
        # transfer new records
        cmd = u&#34;&#34;&#34;
                insert into ref.atc (
                        fk_data_source,
                        code,
                        term,
                        comment,
                        administration_route
                ) select
                        %(src_pk)s,
                        atc,
                        name,
                        nullif(comment, &#39;&#39;),
                        nullif(adro, &#39;&#39;)
                FROM
                        ref.atc_staging
                WHERE
                        not exists (
                                select 1 FROM ref.atc WHERE fk_data_source = %(src_pk)s AND code = ref.atc_staging.atc
                        )
        &#34;&#34;&#34;
        queries.append({&#39;cmd&#39;: cmd, &#39;args&#39;: args})
        # update records so pre-existing ones are refreshed
        cmd = u&#34;&#34;&#34;
                UPDATE ref.atc SET
                        code = r_as.atc,
                        term = r_as.name,
                        comment = nullif(r_as.comment, &#39;&#39;),
                        administration_route = nullif(r_as.adro, &#39;&#39;)
                FROM
                        (SELECT atc, name, comment, adro FROM ref.atc_staging) AS r_as
                WHERE
                        fk_data_source = %(src_pk)s
        &#34;&#34;&#34;
        queries.append({&#39;cmd&#39;: cmd, &#39;args&#39;: args})
        curs = conn.cursor()
        gmPG2.run_rw_queries(link_obj = curs, queries = queries)
        curs.close()
        conn.commit()
        _log.debug(&#39;transfer from ATC staging table to real ATC table done&#39;)

        # clean out staging area
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;delete from ref.atc_staging&#34;&#34;&#34;
        gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd}])
        curs.close()
        conn.commit()
        _log.debug(&#39;ATC staging table emptied&#39;)

        return True

#============================================================
# main
#------------------------------------------------------------
if __name__ == &#34;__main__&#34;:

        if len(sys.argv) == 1:
                sys.exit()

        if sys.argv[1] != &#39;test&#39;:
                sys.exit()

        from Gnumed.pycommon import gmI18N

        gmI18N.activate_locale()
#       gmDateTime.init()

        #--------------------------------------------------------
        def test_atc_import():
                atc_import(cfg_fname = sys.argv[2], conn = gmPG2.get_connection(readonly = False))
        #--------------------------------------------------------
        def test_text2atc():
                print(&#39;searching ATC code for:&#39;, sys.argv[2])
                print(&#39; &#39;, text2atc(sys.argv[2]))
                print(&#39; &#39;, text2atc(sys.argv[2], True))
        #--------------------------------------------------------
        def test_get_reference_atcs():
                print(&#34;reference_of_atc_codes:&#34;)
                for atc in get_reference_atcs():
                        print(atc)
        #--------------------------------------------------------
        #test_atc_import()
        #test_text2atc()
        test_get_reference_atcs()

#============================================================</code></pre>
</details>
</section>
<section>
</section>
<section>
</section>
<section>
<h2 class="section-title" id="header-functions">Functions</h2>
<dl>
<dt id="Gnumed.business.gmATC.atc_import"><code class="name flex">
<span>def <span class="ident">atc_import</span></span>(<span>cfg_fname=None, conn=None)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def atc_import(cfg_fname=None, conn=None):

        # read meta data
        _cfg.add_file_source(source = &#39;atc&#39;, file = cfg_fname, encoding = &#39;utf8&#39;)

        data_fname = os.path.join (
                os.path.dirname(cfg_fname),
                _cfg.get(group = &#39;atc&#39;, option = &#39;data file&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        )                       # must be in same dir as conf file
        version = _cfg.get(group = &#39;atc&#39;, option = &#39;version&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        lang = _cfg.get(group = &#39;atc&#39;, option = &#39;language&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        desc = _cfg.get(group = &#39;atc&#39;, option = &#39;description&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        url = _cfg.get(group = &#39;atc&#39;, option = &#39;url&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        name_long = _cfg.get(group = &#39;atc&#39;, option = &#39;long name&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])
        name_short = _cfg.get(group = &#39;atc&#39;, option = &#39;short name&#39;, source_order = [(&#39;atc&#39;, &#39;return&#39;)])

        _cfg.remove_source(source = &#39;atc&#39;)

        _log.debug(&#39;importing ATC version [%s] (%s) from [%s]&#39;, version, lang, data_fname)

        args = {&#39;ver&#39;: version, &#39;desc&#39;: desc, &#39;url&#39;: url, &#39;name_long&#39;: name_long, &#39;name_short&#39;: name_short, &#39;lang&#39;: lang}

        # find or create data source record
        cmd = u&#34;select pk from ref.data_source where name_short = %(name_short)s and version = %(ver)s&#34;
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])
        if len(rows) &gt; 0:
                data_src_pk = rows[0][0]
                _log.debug(&#39;ATC data source record existed, pk is #%s, refreshing fields&#39;, data_src_pk)
                # exists - update
                args[&#39;pk&#39;] = data_src_pk
                cmd = u&#34;&#34;&#34;UPDATE ref.data_source SET
                                name_long = %(name_long)s,
                                description = %(desc)s,
                                lang = %(lang)s,
                                source = %(url)s
                        WHERE
                                pk = %(pk)s
                &#34;&#34;&#34;
                rows = gmPG2.run_rw_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])
        else:
                _log.debug(&#39;ATC data source record not found, creating&#39;)
                # create
                cmd = u&#34;&#34;&#34;insert into ref.data_source (name_long, name_short, version, description, lang, source) values (
                        %(name_long)s,
                        %(name_short)s,
                        %(ver)s,
                        %(desc)s,
                        %(lang)s,
                        %(url)s
                ) returning pk&#34;&#34;&#34;
                rows = gmPG2.run_rw_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}], return_data = True)
                data_src_pk = rows[0][0]
                _log.debug(&#39;ATC data source record created, pk is #%s&#39;, data_src_pk)

        # import data
        csv_file = open(data_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)
        atc_reader = gmTools.unicode_csv_reader(csv_file, delimiter = &#34;,&#34;, quotechar = &#39;&#34;&#39;)

        # clean out staging area
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;delete from ref.atc_staging&#34;&#34;&#34;
        gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd}])
        curs.close()
        conn.commit()
        _log.debug(&#39;ATC staging table emptied&#39;)

        # from file into staging table
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;insert into ref.atc_staging values (%s, %s, %s, %s, %s)&#34;&#34;&#34;
        first = False
        for atc_line in atc_reader:
                # skip first
                if not first:
                        first = True
                        continue

                # skip blanks
                if atc_line[0] + atc_line[1] + atc_line[2] + atc_line[3] + atc_line[4] == &#39;&#39;:
                        continue

                comment = &#39;&#39;
                unit = &#39;&#39;
                adro = &#39;&#39;

                # &#34;1,1 mg O,P,R,...&#34;
                if regex.match(r&#39;\d{,3},\d{,3}\s.{1,2}\s.(,.)*$&#39;, atc_line[4]):
                        tmp, unit, adro = regex.split(r&#39;\s&#39;, atc_line[4])
                # &#34;1,1 mg O,P,R bezogen auf ...&#34;
                elif regex.match(r&#39;\d{,3},\d{,3}\s.{1,2}\s.(,.)*\s.+$&#39;, atc_line[4]):
                        tmp, unit, adro, comment = regex.split(r&#39;\s&#39;, atc_line[4], 3)
                # &#34;20 mg O&#34;
                elif regex.match(r&#39;\d{,3}\s.{1,2}\s.(,.)*$&#39;, atc_line[4]):
                        tmp, unit, adro = regex.split(r&#39;\s&#39;, atc_line[4])
                # &#34;20 mg O bezogen auf ...&#34;
                elif regex.match(r&#39;\d{,3}\s.{1,2}\s.(,.)*\s.+$&#39;, atc_line[4]):
                        tmp, unit, adro, comment = regex.split(r&#39;\s&#39;, atc_line[4], 3)
                # &#34;Standarddosis: 1 Tablette oder 30 ml Mixtur&#34;
                else:
                        comment = atc_line[4]

                args = [
                        atc_line[0].strip(),
                        atc_line[2],
                        unit,
                        adro,
                        comment
                ]

                gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])

        curs.close()
        conn.commit()
        csv_file.close()
        _log.debug(&#39;ATC staging table loaded&#39;)

        # from staging table to real table
        args = {&#39;src_pk&#39;: data_src_pk}
        queries = []
        # transfer new records
        cmd = u&#34;&#34;&#34;
                insert into ref.atc (
                        fk_data_source,
                        code,
                        term,
                        comment,
                        administration_route
                ) select
                        %(src_pk)s,
                        atc,
                        name,
                        nullif(comment, &#39;&#39;),
                        nullif(adro, &#39;&#39;)
                FROM
                        ref.atc_staging
                WHERE
                        not exists (
                                select 1 FROM ref.atc WHERE fk_data_source = %(src_pk)s AND code = ref.atc_staging.atc
                        )
        &#34;&#34;&#34;
        queries.append({&#39;cmd&#39;: cmd, &#39;args&#39;: args})
        # update records so pre-existing ones are refreshed
        cmd = u&#34;&#34;&#34;
                UPDATE ref.atc SET
                        code = r_as.atc,
                        term = r_as.name,
                        comment = nullif(r_as.comment, &#39;&#39;),
                        administration_route = nullif(r_as.adro, &#39;&#39;)
                FROM
                        (SELECT atc, name, comment, adro FROM ref.atc_staging) AS r_as
                WHERE
                        fk_data_source = %(src_pk)s
        &#34;&#34;&#34;
        queries.append({&#39;cmd&#39;: cmd, &#39;args&#39;: args})
        curs = conn.cursor()
        gmPG2.run_rw_queries(link_obj = curs, queries = queries)
        curs.close()
        conn.commit()
        _log.debug(&#39;transfer from ATC staging table to real ATC table done&#39;)

        # clean out staging area
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;delete from ref.atc_staging&#34;&#34;&#34;
        gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd}])
        curs.close()
        conn.commit()
        _log.debug(&#39;ATC staging table emptied&#39;)

        return True</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmATC.exists_as_atc"><code class="name flex">
<span>def <span class="ident">exists_as_atc</span></span>(<span>substance)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def exists_as_atc(substance):
        args = {&#39;term&#39;: substance}
        cmd = &#39;SELECT EXISTS (SELECT 1 FROM ref.atc WHERE lower(term) = lower(%(term)s))&#39;
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])
        return rows[0][0]</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmATC.get_reference_atcs"><code class="name flex">
<span>def <span class="ident">get_reference_atcs</span></span>(<span>order_by='atc, term, lang')</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def get_reference_atcs(order_by=&#39;atc, term, lang&#39;):
        cmd = &#39;SELECT * FROM ref.v_atc ORDER BY %s&#39; % order_by
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd}])
        return rows</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmATC.propagate_atc"><code class="name flex">
<span>def <span class="ident">propagate_atc</span></span>(<span>substance=None, atc=None, link_obj=None)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def propagate_atc(substance=None, atc=None, link_obj=None):

        _log.debug(&#39;substance &lt;%s&gt;, ATC &lt;%s&gt;&#39;, substance, atc)

        if atc is not None:
                if atc.strip() == &#39;&#39;:
                        atc = None

        if atc is None:
                atcs = text2atc(text = substance, fuzzy = False, link_obj = link_obj)
                if len(atcs) == 0:
                        _log.debug(&#39;no ATC found, aborting&#39;)
                        return atc
                if len(atcs) &gt; 1:
                        _log.debug(&#39;non-unique ATC mapping, aborting&#39;)
                        return atc
                atc = atcs[0][0].strip()

        args = {&#39;atc&#39;: atc, &#39;term&#39;: substance.strip()}
        queries = [
                {&#39;cmd&#39;: &#34;UPDATE ref.substance SET atc = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc IS NULL&#34;,
                 &#39;args&#39;: args},
                {&#39;cmd&#39;: &#34;UPDATE ref.drug_product SET atc_code = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc_code IS NULL&#34;,
                 &#39;args&#39;: args}
        ]
        gmPG2.run_rw_queries(link_obj = link_obj, queries = queries)

        return atc</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmATC.text2atc"><code class="name flex">
<span>def <span class="ident">text2atc</span></span>(<span>text=None, fuzzy=False, link_obj=None)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def text2atc(text=None, fuzzy=False, link_obj=None):

        text = text.strip()

        if fuzzy:
                args = {&#39;term&#39;: &#39;%%%s%%&#39; % text}
                cmd = &#34;&#34;&#34;
                        SELECT DISTINCT ON (atc_code) *
                        FROM (
                                SELECT atc as atc_code, is_group_code, pk_data_source
                                FROM ref.v_atc
                                WHERE term ilike %(term)s AND atc IS NOT NULL
                                        UNION
                                SELECT atc as atc_code, null, null
                                FROM ref.substance
                                WHERE description ilike %(term)s AND atc IS NOT NULL
                                        UNION
                                SELECT atc_code, null, null
                                FROM ref.drug_product
                                WHERE description ilike %(term)s AND atc_code IS NOT NULL
                        ) as tmp
                        ORDER BY atc_code
                &#34;&#34;&#34;
        else:
                args = {&#39;term&#39;: text.casefold()}
                cmd = &#34;&#34;&#34;
                        SELECT DISTINCT ON (atc_code) *
                        FROM (
                                SELECT atc as atc_code, is_group_code, pk_data_source
                                FROM ref.v_atc
                                WHERE lower(term) = lower(%(term)s) AND atc IS NOT NULL
                                        UNION
                                SELECT atc as atc_code, null, null
                                FROM ref.substance
                                WHERE lower(description) = lower(%(term)s) AND atc IS NOT NULL
                                        UNION
                                SELECT atc_code, null, null
                                FROM ref.drug_product
                                WHERE lower(description) = lower(%(term)s) AND atc_code IS NOT NULL
                        ) as tmp
                        ORDER BY atc_code
                &#34;&#34;&#34;

        rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])

        _log.debug(&#39;term: %s =&gt; ATCs: %s (fuzzy: %s)&#39;, text, rows, fuzzy)

        return rows</code></pre>
</details>
</dd>
</dl>
</section>
<section>
</section>
</article>
<nav id="sidebar">
<h1>Index</h1>
<div class="toc">
<ul></ul>
</div>
<ul id="index">
<li><h3>Super-module</h3>
<ul>
<li><code><a title="Gnumed.business" href="http://www.gnumed.de/downloads/docs/api/business/index.html">Gnumed.business</a></code></li>
</ul>
</li>
<li><h3><a href="gmATC.html#header-functions">Functions</a></h3>
<ul class="">
<li><code><a title="Gnumed.business.gmATC.atc_import" href="gmATC.html#Gnumed.business.gmATC.atc_import">atc_import</a></code></li>
<li><code><a title="Gnumed.business.gmATC.exists_as_atc" href="gmATC.html#Gnumed.business.gmATC.exists_as_atc">exists_as_atc</a></code></li>
<li><code><a title="Gnumed.business.gmATC.get_reference_atcs" href="gmATC.html#Gnumed.business.gmATC.get_reference_atcs">get_reference_atcs</a></code></li>
<li><code><a title="Gnumed.business.gmATC.propagate_atc" href="gmATC.html#Gnumed.business.gmATC.propagate_atc">propagate_atc</a></code></li>
<li><code><a title="Gnumed.business.gmATC.text2atc" href="gmATC.html#Gnumed.business.gmATC.text2atc">text2atc</a></code></li>
</ul>
</li>
</ul>
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